Former state chemist Annie Dookhan, who triggered a crisis in the state’s criminal justice system that has set convicted drug dealers free and may cost tens of millions of dollars to fix, is facing a 27-count indictment, Attorney General Martha Coakley’s office said today.

Dookhan, 34, of Franklin, who allegedly mishandled evidence she was supposed to test at a state drug lab, has been indicted by a grand jury on 17 counts of obstruction of justice, as well as 10 other charges, including tampering with evidence, perjury, and falsely pretending to hold a degree from a college or university, prosecutors said.

Dookhan had previously faced criminal charges in Boston Municipal Court. Those will be dropped and the prosecution of the former Department of Public Health employee will now shift to Suffolk Superior Court.

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Dookhan is to be arraigned Thursday in the Boston courthouse.

“We allege that Annie Dookhan tampered with drug evidence and fabricated test results on multiple occasions,” Coakley said in a statement. “Her alleged actions have sent ripple effects throughout the criminal justice system. We are committed to working with all stakeholders to fix this situation and restore trust in the criminal justice system.”

Dookhan worked for the DPH from 2003 until she was fired by the Patrick administration earlier this year. Prosecutors, defense attorneys, and the judicial system have estimated her alleged illegal activities may have undermined thousands of cases. Estimates have ranged from 34,000 to 136,000 cases that were prosecuted during her career.

Prosecutors, the Committee on Public Counsel Services, municipal governments and social service agencies have estimated they will need tens of millions of dollars to deal with the increased caseloads, increased supervision of released defendants, and legal fees stemming from the scandal.

According to Coakley’s statement, Dookhan allegedly “dry labbed’’ seized drugs, falsely certifying that she performed the required testing of seized suspected contraband when, in fact, she had not tested, but had merely made a visual examination.

Dookhan also allegedly tainted samples by mixing substances she knew were illegal drugs with samples she knew did not contain illegal substances. She also allegedly forged the initials of a supervisor on reports in an attempt to cover up her misdeeds, prosecutors allege.

Dookhan occasionally would testify in court as an expert witness and is facing the perjury charge for claiming under oath that she held a master’s degree in chemistry from the University of Massachusetts, when records show she never even enrolled in a master’s program.

These charges are allegations, and the defendant is presumed innocent until proven guilty, prosecutors said.